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- PDB-4idz: Crystal structure of the human fat mass and obesity associated pr... -
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Basic information
Entry | Database: PDB / ID: 4idz | ||||||
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Title | Crystal structure of the human fat mass and obesity associated protein (FTO) in complex with N-oxalylglycine (NOG) | ||||||
![]() | Alpha-ketoglutarate-dependent dioxygenase FTO | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / double-stranded beta helix / jelly-roll motif / oxidoreductase / dioxygenase / nucleic acid demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / oxidative RNA demethylation ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / RNA repair / DNA alkylation repair / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aik, W.S. / McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural basis for inhibition of the fat mass and obesity associated protein (FTO) Authors: Aik, W.S. / Demetriades, M. / Hamdan, M.K.K. / Bagg, E.A.L. / Yeoh, K.K. / Lejeune, C. / Zhang, Z. / McDonough, M.A. / Schofield, C.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.3 KB | Display | ![]() |
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PDB format | ![]() | 151.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 458.2 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ie0C ![]() 4ie4C ![]() 4ie5C ![]() 4ie6C ![]() 4ie7C ![]() 3lfmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56823.047 Da / Num. of mol.: 1 / Fragment: UNP residues 32-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9C0B1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: Chemical | ChemComp-OGA / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.85 % / Mosaicity: 0.988 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG 3350, 85mM trisodium citrate pH5.6, 10% glycerol, 1mM NiCl2, 3mM NOG, 5mM 6-methyladenosine, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 12, 2012 / Details: osmic HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.46→50 Å / Num. all: 22597 / Num. obs: 22286 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 51.11 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.255 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3LFM Resolution: 2.46→26.54 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic
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Displacement parameters | Biso max: 153.96 Å2 / Biso mean: 60.2126 Å2 / Biso min: 29.02 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→26.54 Å
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Refine LS restraints |
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LS refinement shell |
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